Influence of water models on water movement through AQP1

Insights into short chain polyethylene penetration of phospholipid bilayers via atomistic molecular dynamics simulations

The escalation of global plastic production, reaching an annual output of 400 million tons, has significantly intensified concerns regarding plastic waste management. This has been exacerbated by improper recycling and disposal practices, contributing to the impending crisis of plastic pollution. Predictions indicate that by 2025, the environment will bear the burden of over ten billion metric tons of accumulated plastic waste. This situation has led to the concerning release of microplastics and nanoplastics (NPs) into the environment as plastic materials degrade, thereby posing risks to both ecosystems and human health. Nanoparticle interactions with living organisms have garnered significant attention due to their potential to disrupt vital biological processes. Of particular interest are lipid membranes, acting as crucial gatekeepers, underscoring the importance of comprehending the intricate process of NP penetration. Molecular dynamics (MD) simulations serve as a robust tool, offering molecular-level insights into these intricate interactions. In this study, we leverage all-atom MD simulations to delve into the interactions between lipid bilayers and polyethylene (PETH) chains of varying lengths. The investigation spans diverse lipid bilayer compositions-ranging from pure POPC to POPC:DPPC mixtures-revealing how PETH accommodates itself, adopts extended conformations, and influences membrane structure and ordering. Significantly, while longer PETH chains demonstrate limited passive diffusion, their potential to penetrate bilayers over extended timescales emerges as a significant revelation. Overall, this research significantly advances our comprehension of NP-membrane interactions, shedding light on the potential environmental and health implications that lie ahead.

Threonine Cavities Are Targetable Motifs That Control Alpha-Synuclein Fibril Growth

Recent high-resolution structures of alpha-synuclein (aSyn) fibrils offer promise for rational approaches to drug discovery for Parkinson's disease and Lewy body dementia. Harnessing the first such structures, we previously used molecular dynamics and free energy calculations to suggest that threonines 72 and 75─which line water-filled cavities within the fibril stacks─may be of central importance in stabilizing fibrils. Here, we used experimental mutagenesis of both wild-type and A53T aSyn to show that both threonine residues play important but surprisingly disparate roles in fibril nucleation and elongation. The T72A mutant, but not T75A, resulted in a large increase in the extent of fibrillization during primary nucleation, leading us to posit that T72 acts as a "brake" on run-away aggregation. An expanded set of simulations of five recent high-resolution fibril structures suggests that confinement of cavity waters around T72 correlates with this finding. In contrast, the T75A mutation led to a modest decrease in the extent of fibrillization. Furthermore, both T72A and T75A completely blocked the initial fibril elongation in seeded fibrillization. To test whether these threonine-lined cavities are druggable targets, we used computational docking to identify potential small-molecule binders. We show that the top-scoring hit, aprepitant, strongly promotes fibril growth while specifically interacting with aSyn fibrils and not monomer, and we offer speculation as to how such compounds could be used therapeutically.

Novel mechanisms underlying inhibition of inflammation-induced angiogenesis by dexamethasone and gentamicin via PI3K/AKT/NF-κB/VEGF pathways in acute radiation proctitis

Acute radiation proctitis (ARP) is one of the most common complications of pelvic radiotherapy attributed to radiation exposure. The mechanisms of ARP are related to inflammation, angiogenesis, and so on. In this study we evaluated the effect of dexamethasone (DXM) combined with gentamicin (GM) enema on ARP mice, and explored its possible mechanisms by transcriptome sequencing, western blot and immunohistochemistry. C57BL/6 mice were randomly divided into 3 groups: healthy control group, ARP model group, and DXM + GM enema treatment group. ARP mice were established by using a single 6 MV X-ray dose of 27 Gy pelvic local irradiation. Transcriptome sequencing results showed that 979 genes were co-upregulated and 445 genes were co-downregulated in ARP mice compared to healthy mice. According to gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis, we firstly found that PI3K/AKT/NF-κB/VEGF pathways were mostly correlated with the inflammation-induced angiogenesis in ARP mice. PI3K/AKT pathway leads to the activation of NF-κB, which promotes the transcription of VEGF and Bcl-2. Interestingly, symptoms and pathological changes of ARP mice were ameliorated by DXM + GM enema treatment. DXM + GM enema inhibited inflammation by downregulating NF-κB and upregulating AQP3, as well as inhibited angiogenesis by downregulating VEGF and AQP1 in ARP mice. Moreover, DXM + GM enema induced apoptosis by increasing Bax and suppressing Bcl-2. The novel mechanisms may be related to the downregulation of PI3K/AKT/NF-κB/VEGF pathways.